DQ546604
 

Information on mRNA DQ546604

Description: Mus musculus piRNA piR-14716, complete sequence.
Gene: n/a
Product: n/a
Author: Girard,A., Sachidanandam,R., Hannon,G.J. and Carmell,M.A.
Organism: Mus musculus
Tissue: n/a
Development stage: n/a
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-11-02
Version: 1
mRNA sequence: DQ546604
Position: chr12:56958432-56958456

mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |    24  100.0%         12     -  56958432  56958456              DQ546604     1    24    25
browser |    24  100.0%          1     -   5817345   5817369              DQ546604     1    24    25
browser |    24  100.0%          1     -   7678833   7678857              DQ546604     1    24    25
browser |    24  100.0%          1     -   7890054   7890078              DQ546604     1    24    25
browser |    24  100.0%          1     -   8857345   8857369              DQ546604     1    24    25
browser |    24  100.0%          1     +  11439911  11439935              DQ546604     1    24    25
browser |    24  100.0%          1     +  12020678  12020702              DQ546604     1    24    25
browser |    24  100.0%          1     +  18324794  18324818              DQ546604     1    24    25
browser |    24  100.0%          1     -  27176122  27176146              DQ546604     1    24    25
browser |    24  100.0%          1     -  28928604  28928628              DQ546604     1    24    25
browser |    24  100.0%          1     -  29694176  29694200              DQ546604     1    24    25
browser |    24  100.0%          1     +  30728945  30728969              DQ546604     1    24    25
browser |    24  100.0%          1     -  31044671  31044695              DQ546604     1    24    25
browser |    24  100.0%          1     -  31509654  31509678              DQ546604     1    24    25
browser |    24  100.0%          1     +  37322238  37322262              DQ546604     1    24    25
browser |    24  100.0%          1     -  38744347  38744371              DQ546604     1    24    25
browser |    24  100.0%          1     -  41127907  41127931              DQ546604     1    24    25
browser |    24  100.0%          1     -  44399981  44400005              DQ546604     1    24    25
browser |    24  100.0%          1     +  45651966  45651990              DQ546604     1    24    25
browser |    24  100.0%          1     -  47826336  47826360              DQ546604     1    24    25
browser |    24  100.0%          1     +  47997103  47997127              DQ546604     1    24    25
browser |    24  100.0%          1     -  48008794  48008818              DQ546604     1    24    25
browser |    24  100.0%          1     +  48712562  48712586              DQ546604     1    24    25
browser |    24  100.0%          1     -  50199240  50199264              DQ546604     1    24    25
browser |    24  100.0%          1     -  53275280  53275304              DQ546604     1    24    25
browser |    24  100.0%          1     +  57627542  57627566              DQ546604     1    24    25
browser |    24  100.0%          1     +  59388813  59388837              DQ546604     1    24    25
browser |    24  100.0%          1     +  65930828  65930852              DQ546604     1    24    25
browser |    24  100.0%          1     +  67147021  67147045              DQ546604     1    24    25
browser |    24  100.0%          1     +  69742116  69742140              DQ546604     1    24    25
browser |    24  100.0%          1     -  81960781  81960805              DQ546604     1    24    25
browser |    24  100.0%          1     +  86247864  86247888              DQ546604     1    24    25
browser |    24  100.0%          1     -  87388262  87388286              DQ546604     1    24    25
browser |    24  100.0%          1     +  95966112  95966136              DQ546604     1    24    25
browser |    24  100.0%          1     +  96896796  96896820              DQ546604     1    24    25
browser |    24  100.0%          1     +  98530997  98531021              DQ546604     1    24    25
browser |    24  100.0%          1     + 100458939 100458963              DQ546604     1    24    25
browser |    24  100.0%          1     - 103516883 103516907              DQ546604     1    24    25
browser |    24  100.0%          1     - 108065411 108065435              DQ546604     1    24    25
browser |    24  100.0%          1     - 108885043 108885067              DQ546604     1    24    25
browser |    24  100.0%          1     + 112198928 112198952              DQ546604     1    24    25
browser |    24  100.0%          1     + 113609861 113609885              DQ546604     1    24    25
browser |    24  100.0%          1     + 115817882 115817906              DQ546604     1    24    25
browser |    24  100.0%          1     + 117562150 117562174              DQ546604     1    24    25
browser |    24  100.0%          1     + 117677048 117677072              DQ546604     1    24    25
browser |    24  100.0%          1     - 117918378 117918402              DQ546604     1    24    25
browser |    24  100.0%          1     - 128816235 128816259              DQ546604     1    24    25
browser |    24  100.0%          1     - 139652969 139652993              DQ546604     1    24    25
browser |    24  100.0%          1     - 140744959 140744983              DQ546604     1    24    25
browser |    24  100.0%          1     + 142288684 142288708              DQ546604     1    24    25
browser |    24  100.0%          1     + 143725260 143725284              DQ546604     1    24    25
browser |    24  100.0%          1     - 144260292 144260316              DQ546604     1    24    25
browser |    25  100.0%          1     - 150106134 150106159              DQ546604     1    25    25
browser |    24  100.0%          1     + 160648162 160648186              DQ546604     1    24    25
browser |    24  100.0%          1     - 161360360 161360384              DQ546604     1    24    25
browser |    24  100.0%          1     - 166409069 166409093              DQ546604     1    24    25
browser |    24  100.0%          1     - 171658050 171658074              DQ546604     1    24    25
browser |    24  100.0%          1     + 177956636 177956660              DQ546604     1    24    25
browser |    24  100.0%          1     - 179721951 179721975              DQ546604     1    24    25
browser |    24  100.0%          1     - 183297142 183297166              DQ546604     1    24    25
browser |    24  100.0%          1     - 185036291 185036315              DQ546604     1    24    25
browser |    24  100.0%          1     - 191234260 191234284              DQ546604     1    24    25
browser |    24  100.0%          1     - 192312607 192312631              DQ546604     1    24    25
browser |    24  100.0%         10     +   6521061   6521085              DQ546604     1    24    25
browser |    24  100.0%         10     -   7315386   7315410              DQ546604     1    24    25
browser |    24  100.0%         10     +  14488784  14488808              DQ546604     1    24    25
browser |    24  100.0%         10     +  15058842  15058866              DQ546604     1    24    25
browser |    24  100.0%         10     -  15811576  15811600              DQ546604     1    24    25
browser |    24  100.0%         10     -  18115266  18115290              DQ546604     1    24    25
browser |    24  100.0%         10     +  22565964  22565988              DQ546604     1    24    25
browser |    24  100.0%         10     +  26610031  26610055              DQ546604     1    24    25
browser |    24  100.0%         10     -  30357807  30357831              DQ546604     1    24    25
browser |    24  100.0%         10     -  33763242  33763266              DQ546604     1    24    25
browser |    24  100.0%         10     +  34624998  34625022              DQ546604     1    24    25
browser |    24  100.0%         10     +  35600917  35600941              DQ546604     1    24    25
browser |    24  100.0%         10     +  37729535  37729559              DQ546604     1    24    25
browser |    24  100.0%         10     -  38466594  38466618              DQ546604     1    24    25
browser |    24  100.0%         10     +  39640085  39640109              DQ546604     1    24    25
browser |    24  100.0%         10     -  43753605  43753629              DQ546604     1    24    25
browser |    24  100.0%         10     +  47514248  47514272              DQ546604     1    24    25
browser |    24  100.0%         10     +  47559074  47559098              DQ546604     1    24    25
browser |    24  100.0%         10     +  47910439  47910463              DQ546604     1    24    25
browser |    24  100.0%         10     -  54956509  54956533              DQ546604     1    24    25
browser |    24  100.0%         10     +  55596496  55596520              DQ546604     1    24    25
browser |    24  100.0%         10     +  73692699  73692723              DQ546604     1    24    25
browser |    24  100.0%         10     -  74711992  74712016              DQ546604     1    24    25
browser |    24  100.0%         10     -  76756402  76756426              DQ546604     1    24    25
browser |    24  100.0%         10     -  77786977  77787001              DQ546604     1    24    25
browser |    24  100.0%         10     -  77856517  77856541              DQ546604     1    24    25
browser |    24  100.0%         10     +  81513149  81513173              DQ546604     1    24    25
browser |    24  100.0%         10     +  82410509  82410533              DQ546604     1    24    25
browser |    24  100.0%         10     -  82775497  82775521              DQ546604     1    24    25
browser |    24  100.0%         10     +  83308436  83308460              DQ546604     1    24    25
browser |    24  100.0%         10     -  86978631  86978655              DQ546604     1    24    25
browser |    24  100.0%         10     +  91652501  91652525              DQ546604     1    24    25
browser |    24  100.0%         10     -  92355285  92355309              DQ546604     1    24    25
browser |    24  100.0%         10     +  99386790  99386814              DQ546604     1    24    25
browser |    24  100.0%         10     - 103910052 103910076              DQ546604     1    24    25
browser |    24  100.0%         10     + 104413149 104413173              DQ546604     1    24    25
browser |    24  100.0%         10     - 110836516 110836540              DQ546604     1    24    25
browser |    24  100.0%         10     - 121977404 121977428              DQ546604     1    24    25
browser |    24  100.0%         10     - 122341997 122342021              DQ546604     1    24    25
browser |    24  100.0%         10     - 123695672 123695696              DQ546604     1    24    25
browser |    24  100.0%         10     + 124304382 124304406              DQ546604     1    24    25
browser |    24  100.0%         10     - 129050053 129050077              DQ546604     1    24    25
browser |    24  100.0%         11     +   6098210   6098234              DQ546604     1    24    25
browser |    25  100.0%         11     +   7987076   7987101              DQ546604     1    25    25
browser |    24  100.0%         11     +   9036876   9036900              DQ546604     1    24    25
browser |    24  100.0%         11     -  12745944  12745968              DQ546604     1    24    25
browser |    24  100.0%         11     -  13823446  13823470              DQ546604     1    24    25
browser |    24  100.0%         11     +  14849548  14849572              DQ546604     1    24    25
browser |    24  100.0%         11     -  15810357  15810381              DQ546604     1    24    25
browser |    24  100.0%         11     +  16156479  16156503              DQ546604     1    24    25
browser |    24  100.0%         11     -  27084158  27084182              DQ546604     1    24    25
browser |    24  100.0%         11     +  27367197  27367221              DQ546604     1    24    25
browser |    24  100.0%         11     +  29116134  29116158              DQ546604     1    24    25
browser |    24  100.0%         11     -  29230770  29230794              DQ546604     1    24    25
browser |    24  100.0%         11     -  31163334  31163358              DQ546604     1    24    25
browser |    24  100.0%         11     -  31724875  31724899              DQ546604     1    24    25
browser |    24  100.0%         11     -  44275711  44275735              DQ546604     1    24    25
browser |    24  100.0%         11     -  61311623  61311647              DQ546604     1    24    25
browser |    24  100.0%         11     -  67021103  67021127              DQ546604     1    24    25
browser |    24  100.0%         11     +  70959836  70959860              DQ546604     1    24    25
browser |    24  100.0%         11     +  73840313  73840337              DQ546604     1    24    25
browser |    24  100.0%         11     -  74431448  74431472              DQ546604     1    24    25
browser |    24  100.0%         11     +  85332584  85332608              DQ546604     1    24    25
browser |    24  100.0%         11     -  90398970  90398994              DQ546604     1    24    25
browser |    24  100.0%         11     + 104752660 104752684              DQ546604     1    24    25
browser |    24  100.0%         11     - 108541188 108541212              DQ546604     1    24    25
browser |    24  100.0%         11     + 108716574 108716598              DQ546604     1    24    25
browser |    24  100.0%         11     - 113803406 113803430              DQ546604     1    24    25
browser |    24  100.0%         11     - 116650783 116650807              DQ546604     1    24    25
browser |    24  100.0%         11     - 120212313 120212337              DQ546604     1    24    25
browser |    24  100.0%         12     -   4838383   4838407              DQ546604     1    24    25
browser |    24  100.0%         12     -   8453618   8453642              DQ546604     1    24    25
browser |    24  100.0%         12     +  14651006  14651030              DQ546604     1    24    25
browser |    24  100.0%         12     -  17979078  17979102              DQ546604     1    24    25
browser |    24  100.0%         12     -  18010060  18010084              DQ546604     1    24    25
browser |    24  100.0%         12     -  18180497  18180521              DQ546604     1    24    25
browser |    24  100.0%         12     +  19851504  19851528              DQ546604     1    24    25
browser |    24  100.0%         12     +  19867692  19867716              DQ546604     1    24    25
browser |    24  100.0%         12     +  20694845  20694869              DQ546604     1    24    25
browser |    24  100.0%         12     -  21654687  21654711              DQ546604     1    24    25
browser |    24  100.0%         12     -  22092389  22092413              DQ546604     1    24    25
browser |    24  100.0%         12     +  22427397  22427421              DQ546604     1    24    25
browser |    24  100.0%         12     +  23586408  23586432              DQ546604     1    24    25
browser |    24  100.0%         12     +  26158634  26158658              DQ546604     1    24    25
browser |    24  100.0%         12     -  33797699  33797723              DQ546604     1    24    25
browser |    24  100.0%         12     -  35303038  35303062              DQ546604     1    24    25
browser |    24  100.0%         12     -  36666492  36666516              DQ546604     1    24    25
browser |    24  100.0%         12     +  38799270  38799294              DQ546604     1    24    25
browser |    24  100.0%         12     -  39482081  39482105              DQ546604     1    24    25
browser |    24  100.0%         12     -  40232019  40232043              DQ546604     1    24    25
browser |    24  100.0%         12     -  42919893  42919917              DQ546604     1    24    25
browser |    24  100.0%         12     +  44202899  44202923              DQ546604     1    24    25
browser |    24  100.0%         12     +  52222845  52222869              DQ546604     1    24    25
browser |    24  100.0%         12     -  54672231  54672255              DQ546604     1    24    25
browser |    24  100.0%         12     +  60760385  60760409              DQ546604     1    24    25
browser |    24  100.0%         12     +  64202788  64202812              DQ546604     1    24    25
browser |    24  100.0%         12     +  70971512  70971536              DQ546604     1    24    25
browser |    24  100.0%         12     -  79161586  79161610              DQ546604     1    24    25
browser |    24  100.0%         12     +  79615332  79615356              DQ546604     1    24    25
browser |    24  100.0%         12     +  82512715  82512739              DQ546604     1    24    25
browser |    24  100.0%         12     -  91194791  91194815              DQ546604     1    24    25
browser |    24  100.0%         12     +  94010026  94010050              DQ546604     1    24    25
browser |    24  100.0%         12     -  96903885  96903909              DQ546604     1    24    25
browser |    24  100.0%         12     + 101336135 101336159              DQ546604     1    24    25
browser |    24  100.0%         12     + 105273184 105273208              DQ546604     1    24    25
browser |    24  100.0%         12     + 109789160 109789184              DQ546604     1    24    25
browser |    24  100.0%         12     - 112851479 112851503              DQ546604     1    24    25
browser |    24  100.0%         12     + 113164261 113164285              DQ546604     1    24    25
browser |    24  100.0%         12     - 114488596 114488620              DQ546604     1    24    25
browser |    24  100.0%         12     - 114905161 114905185              DQ546604     1    24    25
browser |    24  100.0%         12     - 118318423 118318447              DQ546604     1    24    25
browser |    24  100.0%         12     - 118758833 118758857              DQ546604     1    24    25
browser |    24  100.0%         13     +   3067754   3067778              DQ546604     1    24    25
browser |    24  100.0%         13     -   3665489   3665513              DQ546604     1    24    25
browser |    24  100.0%         13     +   5040171   5040195              DQ546604     1    24    25
browser |    24  100.0%         13     +   6319091   6319115              DQ546604     1    24    25
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browser |    24  100.0%         13     +  11013614  11013638              DQ546604     1    24    25
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browser |    24  100.0%         13     - 102964024 102964048              DQ546604     1    24    25
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browser |    24  100.0%         13     + 106113183 106113207              DQ546604     1    24    25
browser |    24  100.0%         13     - 106275505 106275529              DQ546604     1    24    25
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browser |    24  100.0%         13     - 111636646 111636670              DQ546604     1    24    25
browser |    24  100.0%         13     + 113788274 113788298              DQ546604     1    24    25
browser |    24  100.0%         13     - 116026120 116026144              DQ546604     1    24    25
browser |    24  100.0%         13     - 118286416 118286440              DQ546604     1    24    25
browser |    24  100.0%         13     - 120686449 120686473              DQ546604     1    24    25
browser |    24  100.0%         14     -   3457091   3457115              DQ546604     1    24    25
browser |    24  100.0%         14     -   4323283   4323307              DQ546604     1    24    25
browser |    24  100.0%         14     -   4871659   4871683              DQ546604     1    24    25
browser |    24  100.0%         14     +   5090932   5090956              DQ546604     1    24    25
browser |    24  100.0%         14     +   7005595   7005619              DQ546604     1    24    25
browser |    24  100.0%         14     -   8421547   8421571              DQ546604     1    24    25
browser |    24  100.0%         14     -   8951738   8951762              DQ546604     1    24    25
browser |    24  100.0%         14     +   9642249   9642273              DQ546604     1    24    25
browser |    24  100.0%         14     +  11145658  11145682              DQ546604     1    24    25
browser |    24  100.0%         14     -  15112429  15112453              DQ546604     1    24    25
browser |    24  100.0%         14     -  15569908  15569932              DQ546604     1    24    25
browser |    24  100.0%         14     -  29264853  29264877              DQ546604     1    24    25
browser |    24  100.0%         14     -  29492883  29492907              DQ546604     1    24    25
browser |    24  100.0%         14     -  33370290  33370314              DQ546604     1    24    25
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View details of parts of alignment within browser window
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View table schema

Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

The mRNA track shows alignments between mouse mRNAs in GenBank and the genome.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality.

The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task.

To use the filter:

  1. Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter.
  2. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only mRNAs that match all filter criteria will be highlighted. If "or" is selected, mRNAs that match any one of the filter criteria will be highlighted.
  3. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display mRNAs that match the filter criteria. If "include" is selected, the browser will display only those mRNAs that match the filter criteria.

This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page.

Methods

GenBank mouse mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept.

Credits

The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

References

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518